Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1335 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0914717208 sf0914716207 9 14717208 8.08E-17 NA
vg0122690936 sf0122689891 1 22690936 2.12E-16 3.90E-06
vg0504742919 sf0504742896 5 4742919 3.50E-16 4.61E-06
vg0920030283 sf0920029802 9 20030283 3.97E-16 NA
vg0620601781 sf0620583091 6 20601781 6.15E-16 NA
vg1002992765 sf1002991742 10 2992765 1.57E-15 3.59E-06
vg1013444607 sf1013373377 10 13444607 1.58E-14 7.72E-07
vg0620560057 sf0620559060 6 20560057 1.07E-12 NA
vg0332518144 sf0332511017 3 32518144 NA 1.04E-06
vg1207220741 sf1207218137 12 7220741 NA 6.53E-06